Pathogenic Variant Finder Enhancements

[trevordcampbell]

Pathogenic Variant Finder Enhancements

This PR expands the capabilities of the pathogenic variant finder tool, introducing several new features, improving performance, and enhancing reporting functionality.

New Features

Variant Classification Support

• Added flags to include Variants of Uncertain Significance (VUS) with --include-vus or -v
• Added support for benign variants with --include-benign or -n
• Implemented classification categories for better organization of results

Markdown Report Generation

• Created comprehensive markdown report generation (enabled by default)
• Organized findings by clinical significance categories
• Included variant details with gene-based grouping and proper formatting
• Added sections for methodology, understanding results, and disclaimers

Enhanced Annotation

• Added more complete information from ClinVar
• Improved population frequency data integration from 1000 Genomes
• Better handling of variant classifications and review statuses

Development Environment

• Added DevContainer configuration for consistent development experience
• Improved dependency management
• Added .gitignore for Rust projects

Technical Improvements

Code Quality and Performance

• Fixed ordering of findings in generated CSV and Markdown reports
• Improved error handling throughout the codebase
• Enhanced parallel processing capabilities
• Optimized file downloading with better progress reporting

Documentation

• Added comprehensive technical documentation
• Improved inline code comments
• Updated user-facing documentation
• Added examples and usage instructions

Bug Fixes

• Fixed chromosome ordering in output
• Resolved dependency issues that were causing compilation errors
• Corrected handling of genotype information
• Improved error handling for missing or corrupt files

Other Changes

• General code cleanup and refactoring
• Improved logging throughout the application
• Better progress reporting during long-running operations
• Standardized error types and improved error messages

This PR transforms the tool from a basic pathogenic variant finder to a comprehensive variant analysis tool with flexible classification options and professional reporting capabilities, making it more useful for both clinical and research applications.